PDB-6m96: ATP-bound conformation of the WzmWzt O antigen ABC transporter

ID or keywords:

Entry

Database: PDB / ID: 6m96

Title

ATP-bound conformation of the WzmWzt O antigen ABC transporter

Components

ABC transporter
Transport permease protein

Keywords

MEMBRANE PROTEIN/TRANSPORT PROTEIN / O ANTIGEN / CHANNEL / MEMBRANE PROTEIN / TRANSPORT PROTEIN / MEMBRANE PROTEIN-TRANSPORT PROTEIN complex

Function / homology

Function and homology information

lipopolysaccharide transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Caffalette, C.A. / Zimmer, J.

Citation

Journal: Nat Commun / Year: 2019
Title: A lipid gating mechanism for the channel-forming O antigen ABC transporter.
Authors: Caffalette, C.A. / Corey, R.A. / Sansom, M.S.P. / Stansfeld, P.J. / Zimmer, J.

History

Deposition	Aug 22, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 6, 2019	Provider: repository / Type: Initial release
Revision 2.0	Oct 11, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6m96.cif.gz	254.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6m96.ent.gz	202.2 KB	Display	PDB format
PDBx/mmJSON format	6m96.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6m96_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6m96_full_validation.pdf.gz	1 MB	Display
Data in XML	6m96_validation.xml.gz	28.5 KB	Display
Data in CIF	6m96_validation.cif.gz	40.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/6m96 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/6m96	HTTPS FTP

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Related structure data

Related structure data	6an7 PDB Unreleased entryS 6oih S: Starting model for refinement
Similar structure data	4qqw-1 5byq-d 1kzh-d 1l9b-d 6gm4-d 6xog-d 4qqy-2 3w6w-d 5bys-d 4qqw-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#137 - May 2011 Cytochrome bc1 similarity (1) #123 - Mar 2010 P-glycoprotein similarity (5) #95 - Nov 2007 Multidrug Resistance Transporters similarity (5)

Deposited unit

A: ABC transporter

B: Transport permease protein

hetero molecules

67.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ABC transporter

B: Transport permease protein

hetero molecules

A: ABC transporter

B: Transport permease protein

hetero molecules

defined by author&software
Evidence: homology
136 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	144.751, 144.751, 201.466
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

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Protein , 2 types, 2 molecules AB

#1: Protein	ABC transporter Mass: 27847.365 Da / Num. of mol.: 1 / Fragment: Nucleotide binding domain, residues 3-236 / Mutation: E167Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: abcT4, aq_1094 / Production host: Escherichia coli (E. coli) / References: UniProt: O67181
#2: Protein	Transport permease protein Mass: 30027.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: abcT3, aq_1095 / Production host: Escherichia coli (E. coli) / References: UniProt: O67182

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Non-polymers , 8 types, 417 molecules

#3: Chemical	... ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE Mass: 229.402 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C₁₄H₃₁NO / Comment: LDAO, detergent*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₁H₇₈NO₈P / Comment: DOPE, phospholipid*YM
#8: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#9: Chemical	ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₃
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal grow	Temperature: 290.15 K / Method: vapor diffusion, sitting drop Details: 21-25% PEG 200, 0.02 M sodium acetate pH 4.0, 0.05-0.2 M ammonium sulfate, and 0.02 M sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 4, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9201 Å / Relative weight: 1
Reflection	Resolution: 2.05→25 Å / Num. obs: 78327 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC_1/2: 0.998 / R_pim(I) all: 0.03 / Net I/σ(I): 14.6
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 9.8 % / Num. unique obs: 4396 / CC_1/2: 0.582 / R_pim(I) all: 0.495 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6AN7

6an7
PDB Unreleased entry

Resolution: 2.05→24.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.33

	R_factor	Num. reflection	% reflection
R_free	0.1824	4011	5.13 %
R_work	0.1644	-	-
obs	0.1653	78248	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.05→24.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4040	0	381	371	4792

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4720
X-RAY DIFFRACTION	f_angle_d	0.971	6358
X-RAY DIFFRACTION	f_dihedral_angle_d	7.749	4170
X-RAY DIFFRACTION	f_chiral_restr	0.057	699
X-RAY DIFFRACTION	f_plane_restr	0.005	729

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.0741	0.2891	149	0.2777	2486	X-RAY DIFFRACTION	100
2.0741-2.0994	0.2477	140	0.269	2542	X-RAY DIFFRACTION	100
2.0994-2.126	0.2615	124	0.2488	2511	X-RAY DIFFRACTION	100
2.126-2.1539	0.2547	153	0.2278	2488	X-RAY DIFFRACTION	100
2.1539-2.1834	0.2438	142	0.2183	2502	X-RAY DIFFRACTION	100
2.1834-2.2146	0.2374	130	0.2079	2555	X-RAY DIFFRACTION	100
2.2146-2.2476	0.2045	129	0.2057	2508	X-RAY DIFFRACTION	100
2.2476-2.2827	0.2184	140	0.2016	2532	X-RAY DIFFRACTION	100
2.2827-2.3201	0.1964	123	0.1821	2538	X-RAY DIFFRACTION	100
2.3201-2.3601	0.1867	145	0.1739	2521	X-RAY DIFFRACTION	100
2.3601-2.403	0.2333	154	0.1763	2509	X-RAY DIFFRACTION	100
2.403-2.4491	0.1933	157	0.1678	2521	X-RAY DIFFRACTION	100
2.4491-2.4991	0.1918	124	0.1682	2543	X-RAY DIFFRACTION	100
2.4991-2.5534	0.177	117	0.1595	2569	X-RAY DIFFRACTION	100
2.5534-2.6127	0.1973	138	0.1643	2530	X-RAY DIFFRACTION	100
2.6127-2.678	0.1566	140	0.1557	2548	X-RAY DIFFRACTION	100
2.678-2.7503	0.1619	123	0.1483	2542	X-RAY DIFFRACTION	100
2.7503-2.8311	0.1727	154	0.1495	2536	X-RAY DIFFRACTION	100
2.8311-2.9224	0.1762	146	0.1561	2549	X-RAY DIFFRACTION	100
2.9224-3.0266	0.1733	138	0.1546	2551	X-RAY DIFFRACTION	100
3.0266-3.1476	0.1643	133	0.1547	2581	X-RAY DIFFRACTION	100
3.1476-3.2905	0.1745	155	0.1554	2536	X-RAY DIFFRACTION	100
3.2905-3.4636	0.1651	130	0.146	2590	X-RAY DIFFRACTION	100
3.4636-3.68	0.1715	145	0.1381	2575	X-RAY DIFFRACTION	100
3.68-3.9631	0.1706	141	0.1461	2593	X-RAY DIFFRACTION	100
3.9631-4.3599	0.1679	104	0.1463	2655	X-RAY DIFFRACTION	100
4.3599-4.9864	0.1449	138	0.1348	2631	X-RAY DIFFRACTION	100
4.9864-6.2657	0.207	148	0.1835	2668	X-RAY DIFFRACTION	100
6.2657-24.8815	0.1896	151	0.1925	2827	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.4675	-2.2963	-6.512	3.1361	2.8222	9.5964	-0.6508	-1.0375	-0.3891	0.3939	0.3591	0.2249	0.0669	0.4635	0.2899	0.2883	0.0759	-0.0069	0.3893	0.0214	0.4192	20.7541	61.2286	215.9896
2	2.4687	-0.9835	-1.2018	1.3265	0.6544	1.5424	0.046	0.2925	-0.4676	-0.0832	-0.1462	0.088	0.0899	-0.0631	0.1191	0.3108	0.024	-0.0109	0.3701	-0.1482	0.3905	21.9709	55.178	201.9496
3	6.6596	-1.065	3.7102	3.4877	-1.7376	6.7405	-0.0212	-0.1644	-0.2859	-0.2857	-0.0731	0.207	0.1548	-0.113	0.0617	0.241	0.0017	0.005	0.2846	-0.1524	0.3557	-14.7741	66.8969	210.4851
4	3.6512	0.2691	1.5639	1.7221	-1.4595	4.9187	0.15	-0.2975	-2.1312	-0.0551	0.0674	0.0589	0.8752	0.2144	-0.1701	0.4685	-0.0194	-0.0066	0.3425	-0.0159	0.9123	-8.5185	57.2225	218.9534
5	2.2563	0.0231	-0.3162	3.0043	0.1939	1.833	-0.1272	0.4131	-0.0396	-0.4097	0.1114	0.0361	-0.0168	0.0645	0.011	0.2746	-0.032	-0.0648	0.3725	-0.0997	0.3055	-17.9581	75.6515	205.0203
6	5.298	1.2595	1.0482	2.9319	-0.7735	1.0352	0.004	0.2824	-0.0304	-0.3392	-0.016	-0.0178	0.1053	0.0327	0.0397	0.3385	0.0127	0.0094	0.3444	-0.0743	0.2485	0.3056	86.2331	203.9559
7	5.5138	-4.4044	-4.9922	4.5398	3.8768	4.7294	0.3179	0.969	0.2496	-1.6308	-0.5744	0.0716	-0.8996	-0.406	0.0861	0.6453	0.0078	-0.0336	0.5515	0.0428	0.3261	-0.2833	94.587	194.2869
8	6.3686	1.2698	1.4804	2.8842	0.9297	3.1783	-0.1051	0.4137	0.1291	-0.3297	0.0776	0.0549	-0.1893	0.0946	0.0463	0.28	0.02	-0.0204	0.2343	-0.0046	0.2068	-4.712	93.5821	207.0597
9	2.988	4.7338	3.1408	7.4776	4.9793	3.3323	-0.6724	0.429	1.1468	-1.3172	0.0023	1.4331	-0.8071	-0.4787	0.7495	0.5442	0.0125	-0.2241	0.4573	0.0212	0.5289	-16.6721	97.7555	201.7722
10	4.4755	0.8908	0.4238	5.3743	1.7717	1.7967	0.1101	-0.061	0.4799	-0.3472	0.1592	0.3981	-0.4446	-0.0059	-0.2404	0.3214	0.0333	-0.0711	0.2993	-0.0302	0.4119	-23.2806	89.5148	209.2021
11	7.8116	-3.102	2.3962	3.9415	-4.8619	7.7708	-0.2886	-0.5194	0.3799	0.8326	0.2194	0.8153	-0.743	-0.6367	0.0202	0.3571	0.0094	-0.0194	0.4006	-0.1354	0.4026	-30.1112	80.3179	214.8802
12	9.3496	0.8282	2.3558	8.2369	1.3247	9.7303	0.1568	-0.4398	0.6192	-0.7307	-0.1187	-0.1752	-0.5687	-0.6174	0.0542	0.4349	0.0968	0.116	0.4922	-0.0554	0.4123	9.8844	80.3129	197.1718
13	3.8731	-0.3986	-3.0962	4.4101	4.5743	6.6631	-0.2601	0.7692	-0.1458	0.0865	0.3196	-0.8802	-0.1562	0.1916	-0.0132	0.6578	0.1722	-0.0147	0.7343	-0.1769	0.7477	25.0947	83.211	208.0274
14	6.5973	0.4088	1.4987	6.5076	-1.4463	7.3582	-0.4448	-1.2194	0.6509	0.487	0.6112	-0.6152	-0.1829	0.4111	0.0315	0.4128	0.0405	-0.0216	0.5634	-0.2662	0.4087	43.7329	68.5465	210.5812
15	6.7359	-2.9216	-1.6589	1.0604	0.5023	0.2092	-0.0129	-0.2342	0.1757	-0.1044	0.1084	-0.107	-0.008	0.1173	-0.0842	0.3037	0.0224	0.0031	0.3821	-0.1127	0.3228	21.7754	69.4825	205.8312
16	2.4858	-0.7303	1.191	3.2907	-0.0089	0.568	0.1097	0.5178	-0.3479	-0.453	-0.231	-0.6628	-0.1534	0.1409	0.0986	0.4111	0.0626	0.0992	0.4391	-0.0578	0.4031	26.4157	71.2929	196.0495
17	5.7753	-2.7153	-3.527	1.7901	2.3182	5.5718	0.3726	0.6223	-0.181	-0.2908	-0.2225	-0.0632	-0.3039	0.2336	-0.1822	0.3198	0.06	-0.0603	0.4707	-0.1592	0.3746	19.1177	61.1329	198.7339

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 165 through 182 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 183 through 256 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 0 through 16 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 17 through 40 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 41 through 83 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 84 through 114 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 115 through 129 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 130 through 173 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 174 through 189 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 190 through 207 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 208 through 237 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 16 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 17 through 29 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 30 through 53 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 54 through 98 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 99 through 132 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 133 through 164 )

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